Computational protocol: The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions

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Protocol publication

[…] The RutR-binding motif was extracted from 500-bp DNA sequences centred around the binding peaks using BioProspector (http://ai.stanford.edu/~xsliu/BioProspector/). A DNA sequence logo describing the binding motif was then generated using WebLogo (http://weblogo.berkeley.edu/). For RutR, each of the 20 binding sites identified by ChIP-chip were aligned in PREDetector () and a position weight matrix (PWM) was generated to describe the information content of the binding site. Each target was then assigned a score depending on how it matched the PWM. The average score was used as a cut-off when searching genome sequences for RutR-binding sites. The same approach was used for the other transcription factors shown in except that we used the binding site alignments of Robison et al. () to generate the PWM. […]

Pipeline specifications

Software tools BioProspector, WebLogo, PREDetector
Applications ChIP-on-chip analysis, Genome data visualization
Organisms Escherichia coli